Fig. 1: Co-transcriptionally formed R-loop promotes FLC chromatin silencing.

a S9.6-DNA/RNA immunoprecipitation (DRIP)-qPCR analyzing the R-loop over 3′-end of FLC in wild-type Col-0, with and without RNase H treatment. The number on x axis is the distance to FLC transcription start site (TSS = 0), and x axis is corresponding to the schematic on the top. TTS transcription termination site. Data are mean ± s.e.m. from three independent experiments. b Expression of spliced FLC relative to UBC in various genetic backgrounds. Data are normalized to wild-type Col-0. Data are mean ± s.e.m. from three to five biological replicates. Two-tailed P value from multiple t test corrected by Holm–Sidak method. c FCA–RIP–qPCR analyzing FCA enrichment on COOLAIR transcript in Col-0, ndx1-4 and fca-9 (negative control). The number on x axis is the distance to COOLAIR 5′-end. Data are mean ± s.e.m. from three biological replicates. d ChIP analysis of H3K4me1 level at FLC in various genetic backgrounds. The number on x axis is the distance to FLC TSS. Data are mean ± s.d. from three biological replicates. e DRIP–qPCR analyzing the R-loop in Fig. 1a (COOLAIR R-loop) in Col-0 and mutants fca-9 and fld-4. Data are mean ± s.e.m. from three biological replicates. f DRIP–qPCR analyzing the COOLAIR R-loop in Col-0 and fy-2. Data are mean ± s.e.m. from three biological replicates. Source data are provided as a Source Data file.